Hi, I am having a problem with write.nexus.data, such that the file generated is nonsense.
I have a very, very large data set, but have been working with a subset trying to solve this problem. My data is in .fasta format, and I am looking to convert it into nexus format. I load the data: > library(ape) > data <- read.dna("concat.fasta", format="fasta", as.matrix=TRUE) This gives the following: > data > 5 DNA sequences in binary format stored in a matrix All sequences of same length: 5023 Labels: Species etc. Base composition: a c g t Also: > class(data) > "DNAbin" This is exactly the same as the woodmouse example data provided in the package ape, which I have been following when trying to solve this issue (see ?write.nexus.data). When I export the data: > write.nexus.data(data, file="test.nex", interleaved=TRUE, charsperline=100) a file is produced which begins: BEGIN DATA; DIMENSIONS NTAX=135165 NCHAR=1; FORMAT DATATYPE=DNA MISSING=? GAP=- INTERLEAVE=YES; MATRIX 1 04000000000 etc. I haven't been able to find other posts on this, any help is greatly appreciated. Sincerely, Nick -- Nicholas Crouch Graduate Student, Igić Lab Department of Biological Sciences University of Illinois at Chicago [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/